[2] After the fall of Obote in July 1984/5, over 1,000 cadres of the UNRF joined Yoweri Museveni's government.

In April 1990 he was arrested on treason charges, and incarcerated until June 1992, when he was released and acquitted.

It operated mostly in Aringa County, Arua District, out of bases in southern Sudan, and received support from the Sudanese government (the National Islamic Front), in retaliation for Ugandan government's support for the Sudan People's Liberation Army.

On December 24, 2002, the UNRF II signed a formal ceasefire with the government in the town of Yumbe in northwestern Uganda.

The terms included a battalion of UNRF II soldiers being incorporated into the Ugandan army, and USh 4.2 billion being distributed to the group.